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Table 2 Results of RIEMS validation using our simulated sample dataset with original (upper half) and deviating (lower half) sequences

From: RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Input species True positive False positive True negative False negative Unclassified Sensitivity Specificity Positive predictive value Negative predicitive value Correct classification rate False classification rate
Original sequences            
Bacillus anthracis 12774 731 76880 0 0 100 99.06 94.59 100 99.19 0.81
Burkholderia mallei 16092 102 74129 62 0 99.62 99.86 99.37 99.92 99.82 0.18
Clostridium botulinum 12300 0 77649 436 0 96.58 100 100 99.44 99.52 0.48
Staphylococcus aureus 12425 0 77678 282 0 97.78 100 100 99.64 99.69 0.31
Escherichia coli 12289 0 77761 335 0 97.35 100 100 99.57 99.63 0.37
Yersinia pestis 12551 0 77788 46 0 99.63 100 100 99.94 99.95 0.05
Newcastle disease virus 418 0 89967 0 0 100 100 100 100 100 0
Akabane virus 119 0 90266 0 0 100 100 100 100 100 0
Influenza A virus 1 0 90384 0 0 100 100 100 100 100 0
Bos taurus 4906 0 85476 3 2 99.94 100 100 100 100 0
Canis lupus 5346 0 85039 0 0 100 100 100 100 100 0
Deviating sequences            
Bacillus anthracis 12762 633 76978 12 0 99.91 99.18 95.27 99.98 99.29 0.71
Burkholderia mallei 16055 79 74152 99 0 99.39 99.89 99.51 99.87 99.8 0.2
Clostridium botulinum 12358 1 77648 378 0 97.03 100 99.99 99.52 99.58 0.42
Staphylococcus aureus 12484 1 77677 223 0 98.25 100 99.99 99.71 99.75 0.25
Escherichia coli 12400 0 77761 224 1 98.23 100 100 99.71 99.75 0.25
Yersinia pestis 12529 0 77788 68 1 99.46 100 100 99.91 99.92 0.08
Newcastle disease virus 418 0 89967 0 0 100 100 100 100 100 0
Akabane virus 119 0 90266 0 0 100 100 100 100 100 0
Influenza A virus 1 0 90384 0 0 100 100 100 100 100 0
Bos taurus 4887 0 85476 22 5 99.55 100 100 99.97 99.98 0.02
Canis lupus 5346 0 85039 0 0 100 100 100 100 100 0